Plant growth-promoting rhizobacteria (PGPR) are generally referred to as a heterogeneous group of bacteria which colonize the rhizoplane and/or rhizosphere and stimulate plant growth [1
]. PGPR have been commercially exploited as biofertilizers to improve the yield of crops. Some PGPR have also been successfully used as biocontrol agents to prevent plant diseases caused by phytopathogens, especially some soil-borne diseases [3
]. The investigations on the interactions between PGPR and their host plants can not only contribute to our understanding of eukaryote-prokaryote relationships, but also have fundamental implications for designing new strategies to promote agricultural plant production.
In recent years, there is increasing evidence that plant root exudates play a key role in plant-microbe interactions [6
]. Root exudates consist of an enormous range of compounds, among which some can attract beneficial associative bacteria to overcome stress situations [8
]. On the other hand, root exudates contain low molecular-weight carbon such as sugars and organic acids that primarily act as energy sources for rhizobacteria and shape bacterial communities in the rhizosphere [11
]. To date, however, it remains unclear how root exudates exert differential effects on rhizobacteria and which mechanisms or pathways make rhizobacteria responsive to plant root exudates.
Transcriptome analyses are an efficient approach to study host-microbe interactions at a wider scale. So far, the use of this approach to analyse bacterial gene expression has been extensively used to study pathogenic microbes infecting their host [12
]. Only a few studies were performed with beneficial PGPR [13
]. Several genes from Pseudomonas aeruginosa
involved in metabolism, chemotaxis and type II secretion were identified to respond to sugar-beet root exudates [13
]. In another study, it has been suggested that the availability of particular metabolites in root exudates, especially amino acids and aromatic compounds, support Pseudomonas putida
to colonize the rhizosphere [14
]. Rhizobium leguminosarum
was grown in the rhizospheres of its host-legume pea and two other non-host plants, alfalfa and sugar-beet. Although numerous sugar and putative complex carbohydrate transport systems are induced in the rhizosphere, they are less important carbon sources than organic acids. A common core of rhizosphere-induced genes was identified [15
So far, studies on the impact of root exudates on PGPR, have been conducted with Gram-negative bacteria, mainly Azospirillum
]. Related studies performed with Gram-positive PGPR are still missing. Owing to differences in lifestyle and physiology, Gram-positive and Gram-negative rhizobacteria may use distinct mechanisms when interacting with plants. Due to their ability to produce durable endo-spores, bacilli are now preferred in manufacturing biofertilizer formulations [18
], however, their successful application is still hampered by a lack of knowledge about factors determining interactions between plants and those bacteria, especially root colonization is far from being completely understood.
FZB42 is a plant root-colonizing Gram-positive PGPR. A series of studies has elucidated several aspects of this rhizobacterium, particularly the molecular basis of its plant growth-promoting activity, which is mainly based on the production of secondary metabolites suppressing competitive microbial pathogens occurring in the plant rhizosphere, the secretion of the plant growth hormone auxin, and the synthesis of volatiles stimulating plant growth and induced systemic resistance (ISR) [19
]. In the case of Gram-positive PGPR, however, it is still not clear how they maneuver their gene expression when exposed to plant-derived compounds. To address this question, the commercially established FZB42 wild type strain from Bacillus amyloliqufaciens
was tested in this study for its transcriptomic responses to maize root exudates using a two-color DNA microarray system.